How were some people banned? I don't know the details, but it was the result of a lot of work by Jagex moderators over a period of months, that started with them going in game, it involves either some form of spying, or detailed manual analysis of in-game activity.
The trick to getting to 99 and beyond is use the program when it's safe. Can a bot be completely safe for all time, no matter how much study is put in by those trying to detect it? Yes, but there's more work that needs done before this level is reached. Jagex are working hard trying to find ways to detect this bot, in a way they don't with other bots.
In a few weeks time there will be a revamped MTA bot, and then not long after that, the PC bot will be released.